"Raul Castro thanked the Pope for his mediation between Cuba and the United States," said Vatican spokesman Federico Lombardi of the exchange that also focused on Francis' upcoming visit to Cuba.
The first South American pope played a key role in secret negotiations between the United States and Cuba, which led to the surprise announcement in December that the two countries would seek to restore diplomatic ties after more than 50 years of tensions.
Francis in turn presented Castro a medal of Saint Martin de Tours, a French saint celebrated for having given his coat to a beggar, and urged others to "clothe and support the poor."
Castro, who was accompanied by his Foreign Minister Bruno Rodriguez Parrilla, held a private hour-long meeting with the pontiff in a small room adjoining the Paul VI Audience Hall, where large gatherings are held in the Vatican.
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Castro said he was "very struck" by the Catholic leader's "modesty and wisdom" and promised to attend all the masses given by Francis on his Cuba visit in September.
"I read all the Holy Father's speeches," Castro said, adding that if the pope "continues to speak in this way, one day I will start praying again and return to the Catholic Church. And I'm not saying that as a joke."
Pope Francis arrived ten minutes ahead of Castro.
A dozen uniformed Swiss Guards stood to attention in front of the building when the limousine bearing the Cuban flag arrived.
The Vatican announced last month that Pope Francis would visit the Caribbean island in September, becoming only the third pontiff to do so after John Paul II in 1998 and Benedict XVI in 2012.
Jorge Bergoglio, then auxiliary bishop of Buenos Aires and now Pope Francis, accompanied John Paul II on the first papal visit to Cuba, during which John Paul II called for Havana to be brought in from the cold.
"Let Cuba open itself to the world, and let the world open itself to Cuba," he urged, two years after hosting Castro's ailing older brother Fidel for talks at the Vatican.